1) rpg maker has many ways to fix the "test a longer game" like fighting boss with items and stats for that boss. You can teleport your player with the given stuff to make sure things run, etc. This isn't a problem with testing longer game it is a problem of not using rpg maker tools to test things.
2) Nothing gets broken unless you mix plugins with plugins that do the same things or bad programing within plugin. RPG maker is made to run in almost anywhere. The only known errors that might ruin your game from RPG Maker series are new updates that might break your game.
3) This is a common problem but not something people do a lot in rpg maker.
All this just seems to be your problem reather than everyone problem. New people could face these problems but even they try to keep a game neat. I never heard people complain about rpg makers having bad programing or errors it's just people complain about rpg maker being easy for people to make games.